Measuring the factors that determine water quality can help to evaluate the health of an ecosystem. Water quality testing monitors the concentration of various chemical components and there are relationships between several of the chemical tests (i.e. oxygen and carbon dioxide, carbon dioxide and pH, carbon dioxide and alkalinity).

Dissolved Oxygen comes from green plants in the water, wind and wave action and from the bubbling action of rapids and waterfalls. Oxygen is necessary to the survival of almost all life and is one of the most important chemical parameters to measure. Oxygen levels vary greatly throughout the day, peaking towards mid-afternoon and tapering off towards nightfall. Also, large amounts of oxygen are required by the bacteria which aid in decomposition and large quantities of dead material will deplete available oxygen.

High oxygen-demanding (intolerant) organisms can only withstand good water quality, while tolerant organisms can withstand poor water quality. For example "blood worms" appear red due to high haemoglobin levels. They are efficient at absorbing oxygen from their environment in the bottom sediments.

Carbon Dioxide, like dissolved oxygen, is used to determine the quality of aquatic ecosystems.

The major sources of carbon dioxide in water are the atmosphere, rainfall, soil, respiration of plants and animals, and decomposition. High levels of carbon dioxide (25 mg/l to 50 mg/l) will kill animal life while low levels (below 50 ppm) will kill plant life.

Carbon dioxide values change throughout the day. Because photosynthesis stops at night, carbon dioxide is produced through respiration. When photosynthesis resumes in the morning, carbon dioxide is used up.

pH describes how alkaline or acid a solution is. It is simply a measurement of the concentration of hydrogen ions in solution and is expressed on a scale ranging from 0 to 14. On this scale, 7 is neutral (neither acidic or basic), below 7 is acidic, and above 7 is basic (or alkaline). The scale is logarithmic, that means a solution of pH 4 is 10 times more acidic than a pH 5 solution, and a solution with a pH of 3 is 100 times more acidic than a solution with pH 5.

Most aquatic species need a pH range between 5 and 9. Few species can tolerate conditions below or above this range. Short-term exposure to low pH levels may cause sudden death, or stress leading to death. For example, a low pH interferes with the gaseous exchange in fish (the ability to receive oxygen in the gills), and breathing. Low or high pH may affect sperm motility, egg division or egg hatching.

Many waterbodies do become more acidic as they age. As a waterbody becomes more acidic, the productivity is reduced. An example of the phenomenon is found when comparing a marsh to a bog. Marshes are relatively young with a neutral to basic pH, supporting a great diversity of flora and fauna. Acidic bogs, on the other hand, support specific organisms adapted to a low pH environment.

Testing the pH will help to determine if the water is suitable for aquatic species, if there are signs of pollution (especially acid rain) and aspects of the productivity of the waterbody.

Nitrates are essential in the formation of proteins and are therefore an important nutrient for all living organisms. Nitrates act as a link in the nitrogen cycle, eventually being used as a plant nutrient. Living organisms such as blue-green algae, bacteria, and leguminous (nitrogen-fixing) plants have the ability to convert nitrogen into a more usable form.

However, in systems without oxygen, the normal nitrogen cycle causes an ammonia build-up (normally the ammonia would change chemically into a less-lethal nitrates). Ammonia is toxic, the lethal limit being .5 mg/l. Nitrites are also toxic, but rarely abundant. Levels for nitrates in an aquatic ecosystem reach a limit of 4-5 mg/l. Because nitrates are constantly absorbed by plant materials, there is rarely any accumulation. High levels are usually the result of sewage input, runoff from cattle feed lots (urine), waste material from aquatic birds or the decomposition of organic material.

Phosphates, as part of the phosphate cycle, are important for photosynthesis and cellular respiration. In nature, phosphates are cycled from igneous rock and natural phosphate deposits, by weathering, leaching, and erosion. In the presence of water phosphates adhere to soil particles but, once decayed, become available to plants.

Phosphorus is usually the limiting nutrient for aquatic organisms because it is found in such small quantities. Excess phosphates come from human sources including detergents, feedlots, fertilizers, and sewage. High levels of phosphates are often responsible for algal blooms. This overabundant growth of algae produces a thick green scum covering the surface of the water. When this algae decomposes, oxygen levels decrease and aquatic organisms die. Acceptable phosphate levels in an aquatic ecosystem are below 0.025 mg/l. Anything above this amount could result in an algal bloom.

Chlorides - The amount of chlorides in a body of freshwater determined by the nearness of natural sources, such as igneous rock and volcanic gases or similar sources. Otherwise, the major source of chlorides are human-related. When conducting chloride tests, check the area for nearby sewage treatment plants or sewers. If the tests exceed the normal limit, in all likelihood, there is a subsurface seepage from septic tanks introducing soluble chloride salts. One other important human source is the winter salting of streets and highways. Spring run-off and meltwater containing soluble salts can be carried into aquatic ecosystems. In amphibians, high chloride levels cause respiratory failure and possible osmoregulatory imbalances.